The self-assembly of nucleic acid bases on metal and mineral surfaces

Thesis

The ability of RNA bases to self-assemble into larger structures is an important research area relevant to the origins of life. In the RNA helix the bases are arranged on a sugar-phosphate carcass but it has been suggested that the initial ordering could form on a flat surface. This thesis is an attempt to establish experimentally whether the complementary RNA bases, adenine and uracil, have the ability to self-assemble into large ordered structures when adsorbed on metal and mineral surfaces. The Au (111) surface was chosen as a preferred substrate as it is flat, relatively free of defects, chemically inert and reconstructs in a characteristic pattern of corrugation lines, which provide a reference for crystallographic directions. Six of the molecular phases shown were observed for the first time with molecular resolution and the possible two-dimensional arrangements of adenine and uracil molecules for these phases are proposed. The pure adenine and pure uracil structures have chiral unit cells and in the case of pure uracil alternating monochiral domains within the polychiral islands are created. Well-ordered intricate uracil-adenine bimolecular networks were also observed. The self-assembly of both uracil and adenine appears to be weakly influenced by the surface crystallography. The (100) surface of the mineral pyrite (FeS₂) was chosen as the alternative substrate as it is the most common face that occurs naturally in pyrite crystals. The experiments show the formation of small adenine and uracil crystals at the terrace edges. Neither uracil nor adenine were observed to form a monolayer on the surface of the terraces. The results of the experiments described in this thesis are very interesting in terms of establishing the possible mechanisms for creating regular chiral molecular networks and provide a useful insight into the role of surfaces in the processes of self-assembly of RNA bases.

Authors: Shvarova, O; Olga Y Shvarova

• Publication date: 2011
• DOI: 10.5287/ora-xv85v5nvm
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: Oxford University, UK
• Language: English
• Keywords: molecular self-assembly; gold (111); self-assembly; STM; adenine; RNA; origin of life; uracil; pyrite (100); Au (111); scanning tunneling microscopy; nucleic bases
• Subjects: Scanning tunnelling microscopy; Microscopy and microanalysis; Surface nanoscience; Atomic scale structure and properties; Surfaces; Electron image analysis